Last year, Jack Lenz’s team at the Albert Einstein College of Medicine in New York began looking for signs of endogenous retroviruses in the ancient genomes, a class of virus that not only invades cells but worms its way into DNA. These retroviral gene sequences make up about 8 per cent of the human genome, and are part of what is sometimes called “junk” or non-coding DNA because they don’t contain genetic instructions to make proteins.

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Lenz found 14 retroviral gene sequences in the Neanderthal and Denisovan DNA. When he compared this to the human genome used as a standard reference, he found that none of the sequences overlapped – in other words, it seemed that modern humans did not share this endogenous retroviral DNA with their extinct cousins.

Not so fast

That was until Robert Belshaw at Plymouth University, UK, and Gkikas Magiorkinis at the University of Oxford, who study whether these viral DNA sequences contribute to disease, decided to take a closer look.

They examined the genomes of 67 people with cancer, and found they contained six of the sequences supposedly unique to the ancient humans. Belshaw suspects that all 14 might still be around, although finding the rest will take more time. The viruses insert themselves into DNA repeats – patterns that occur in multiple locations throughout the genome, only one of which will carry the sequence in question, so tracking them down is time consuming.

The finding suggests that the viruses probably infected our ancestors before we split from the lineage that led to Neanderthals and Denisovans, roughly 400,000 years ago.

So why did Lenz’s team miss the retroviral sequences in humans?

Everyone is different

“They were looking for them in what we call the human reference genome,” says Belshaw. This is built up using information from many individuals, but any given position in that genome contains information from just one person. By chance, the regions of the reference genome that Lenz’s team studied happened to have come from individuals who lack the endogenous retrovirus sequences found in the Neanderthal and Denisovan DNA.

The new study is important, says Magiorkinis, because it emphasises that modern humans can differ from one another significantly in the non-coding parts of their genomes. “The results show that we can find individuals today who share loci with Denisovans or Neanderthals, but not with other humans alive today,” he says.

This shows how vital it is to know whether an individual possesses or lacks a certain sequence rather than just assuming it is present, says Jonathan Stoye at the MRC National Institute for Medical Research in London. “Such properly analysed data will be necessary to establish whether there is any real link between endogenous retroviruses and disease,” he says.

Belshaw and Magiorkinis’s team is now exploring just how widespread this retroviral DNA is in the modern human population and whether the viruses themselves are ever active. “Within the next five years, we should be able to say for sure whether these ancient viruses play a role in modern human diseases,” says Belshaw.